The Digital Inspiration blog has a really thorough checklist, with links to relevant, free software to help you back up and get your system back up to a fully-patched, optimized state.

Note the tip at the very end, involving a can of compressed air, because it's a worthy one, in my experience. While you've already got your system on the lifts, so to speak, it pays to blast away the CPU-heating, fan-clogging bunnies in there. For desktop systems, Gina's got a great explanatory feature on how to do just that.